logo

Chinese Science Bulletin, Volume 64 , Issue 10 : 1027-1036(2019) https://doi.org/10.1360/N972018-00874

DNAzymes in biological detection and gene therapy

More info
  • ReceivedAug 24, 2018
  • AcceptedOct 9, 2018
  • PublishedNov 23, 2018

Abstract


Funded by

国家自然科学基金优秀青年科学基金(81822024)

国家自然科学基金国际合作项目(11761141006)

国家自然科学基金(21605102)

国家重点研发计划生物安全专项(2017YFC1200904)


Supplement

补充材料

图S1 Pb2+ DNAzyme的二级结构

图S2 UO22+ DNAzyme

图S3 基于L-组氨酸依赖性的DNAzyme检测体系构建

本文以上补充材料见网络版csb.scichina.com. 补充材料为作者提供的原始数据, 作者对其学术质量和内容负责.


References

[1] Lander E S, Linton L M, Birren B, et al. Initial sequencing and analysis of the human genome. Nature, 2001, 409: 860-921 CrossRef Google Scholar

[2] E. Wang R, Zhang Y, Cai J, et al. Aptamer-based fluorescent biosensors. CMC, 2011, 18: 4175-4184 CrossRef Google Scholar

[3] Achenbach J, Chiuman W, Cruz R, et al. Dnazymes: From creation in vitro to application in vivo. CPB, 2004, 5: 321-336 CrossRef Google Scholar

[4] Silverman S K. In vitro selection, characterization, and application of deoxyribozymes that cleave RNA. Nucleic Acids Res, 2005, 33: 6151-6163 CrossRef Google Scholar

[5] Wang F, Lu C H, Willner I. From Cascaded Catalytic Nucleic Acids to Enzyme–DNA Nanostructures: Controlling Reactivity, Sensing, Logic Operations, and Assembly of Complex Structures. Chem Rev, 2014, 114: 2881-2941 CrossRef Google Scholar

[6] Sullenger B A, Gilboa E. Emerging clinical applications of RNA. Nature, 2002, 418: 252-258 CrossRef ADS Google Scholar

[7] Pelossof G, Tel-Vered R, Willner I. Amplified Surface Plasmon Resonance and Electrochemical Detection of Pb2+ Ions Using the Pb2+-Dependent DNAzyme and Hemin/G-Quadruplex as a Label. Anal Chem, 2012, 84: 3703-3709 CrossRef Google Scholar

[8] Needleman H. Lead poisoning. Annu Rev Med, 2004, 55: 209-222 CrossRef Google Scholar

[9] Baker A S, Deiters A. Optical control of protein function through unnatural amino acid mutagenesis and other optogenetic approaches. ACS Chem Biol, 2014, 9: 1398-1407 CrossRef Google Scholar

[10] Kumar B N, Venkata Ramana D K, Harinath Y, et al. Separation and Preconcentration of Cd(II), Cu(II), Ni(II), and Pb(II) in Water and Food Samples Using Amberlite XAD-2 Functionalized with 3-(2-Nitrophenyl)-1 H-1,2,4-triazole-5(4 H )-thione and Determination by Inductively Coupled Plasma–Atomic Emission Spectrometry. J Agric Food Chem, 2011, 59: 11352-11358 CrossRef Google Scholar

[11] Wegner S V, Okesli A, Chen P, et al. Design of an Emission Ratiometric Biosensor from MerR Family Proteins:  A Sensitive and Selective Sensor for Hg2+. J Am Chem Soc, 2007, 129: 3474-3475 CrossRef Google Scholar

[12] Peng X, Du J, Fan J, et al. A Selective Fluorescent Sensor for Imaging Cd2+ in Living Cells. J Am Chem Soc, 2007, 129: 1500-1501 CrossRef Google Scholar

[13] Vester B, Wengel J. LNA (Locked Nucleic Acid):  High-Affinity Targeting of Complementary RNA and DNA. Biochemistry, 2004, 43: 13233-13241 CrossRef Google Scholar

[14] Yang H, Zhou Z, Huang K, et al. Multisignaling Optical-Electrochemical Sensor for Hg2+ Based on a Rhodamine Derivative with a Ferrocene Unit. Org Lett, 2007, 9: 4729-4732 CrossRef Google Scholar

[15] Breaker R R, Joyce G F. A DNA enzyme that cleaves RNA. Chem Biol, 1994, 1: 223-229 CrossRef Google Scholar

[16] Olea Jr. C, Horning D P, Joyce G F. Ligand-Dependent Exponential Amplification of a Self-Replicatingl-RNA Enzyme. J Am Chem Soc, 2012, 134: 8050-8053 CrossRef Google Scholar

[17] Lu L M, Zhang X B, Kong R M, et al. A ligation-triggered dnazyme cascade for amplified fluorescence detection of biological small molecules with zero-background signal. J Am Chem Soc, 2011, 133: 11686-11691 CrossRef Google Scholar

[18] Liu X, Tang Y, Wang L, et al. Optical detection of mercury(ii) in aqueous solutions by using conjugated polymers and label-free oligonucleotides. Adv Mater, 2007, 19: 1471-1474 CrossRef Google Scholar

[19] Liu J, Lu Y. Adenosine-dependent assembly of aptazyme-functionalized gold nanoparticles and its application as a colorimetric biosensor. Anal Chem, 2004, 76: 1627-1632 CrossRef Google Scholar

[20] Liu J, Lu Y. Improving fluorescent dnazyme biosensors by combining inter- and intramolecular quenchers. Anal Chem, 2003, 75: 6666-6672 CrossRef Google Scholar

[21] Zhang X B, Wang Z, Xing H, et al. Catalytic and molecular beacons for amplified detection of metal ions and organic molecules with high sensitivity. Anal Chem, 2010, 82: 5005-5011 CrossRef Google Scholar

[22] Li H, Zhang Q, Cai Y, et al. Single-stranded dnazyme-based Pb2+ fluorescent sensor that can work well over a wide temperature range. Biosens Bioelectron, 2012, 34: 159-164 CrossRef Google Scholar

[23] Xu W, Tian J, Luo Y, et al. A rapid and visual turn-off sensor for detecting copper (II) ion based on DNAzyme coupled with HCR-based HRP concatemers. Sci Rep, 2017, 7: 43362 CrossRef ADS Google Scholar

[24] Liu J, Lu Y. A DNAzyme Catalytic Beacon Sensor for Paramagnetic Cu2+ Ions in Aqueous Solution with High Sensitivity and Selectivity. J Am Chem Soc, 2007, 129: 9838-9839 CrossRef Google Scholar

[25] Li H, Huang X X, Kong D M, et al. Ultrasensitive, high temperature and ionic strength variation-tolerant Cu2+ fluorescent sensor based on reconstructed Cu2+-dependent DNAzyme/substratecomplex. Biosens Bioelectron, 2013, 42: 225-228 CrossRef Google Scholar

[26] Cui L, Peng R, Fu T, et al. Biostable l-DNAzyme for sensing of metal ions in biological systems. Anal Chem, 2016, 88: 1850-1855 CrossRef Google Scholar

[27] Liu J, Lu Y. A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. J Am Chem Soc, 2003, 125: 6642-6643 CrossRef Google Scholar

[28] Mei S H J, Liu Z, Brennan J D, et al. An efficient RNA-cleaving DNA enzyme that synchronizes catalysis with fluorescence signaling. J Am Chem Soc, 2003, 125: 412-420 CrossRef Google Scholar

[29] Kandadai S A, Li Y. Characterization of a catalytically efficient acidic RNA-cleaving deoxyribozyme. Nucleic Acids Res, 2005, 33: 7164-7175 CrossRef Google Scholar

[30] Ali M M, Kandadai S A, Li Y. Characterization of pH3DZ1 — An RNA-cleaving deoxyribozyme with optimal activity at pH 3. Can J Chem, 2007, 85: 261-273 CrossRef Google Scholar

[31] Aguirre S D, Ali M M, Kanda P, et al. Detection of bacteria using fluorogenic dnazymes. J Vis Exp, 2012, 3961. Google Scholar

[32] Ali M M, Aguirre S D, Lazim H, et al. Fluorogenic dnazyme probes as bacterial indicators. Angew Chem Int Ed, 2011, 50: 3751-3754 CrossRef Google Scholar

[33] Zhang W, Feng Q, Chang D, et al. In vitro selection of RNA-cleaving dnazymes for bacterial detection. Methods, 2016, 106: 66-75 CrossRef Google Scholar

[34] Yousefi H, Ali M M, Su H M, et al. Sentinel wraps: Real-time monitoring of food contamination by printing dnazyme probes on food packaging. ACS Nano, 2018, 12: 3287-3294 CrossRef Google Scholar

[35] He S, Qu L, Shen Z, et al. Highly specific recognition of breast tumors by an RNA-cleaving fluorogenic dnazyme probe. Anal Chem, 2015, 87: 569-577 CrossRef Google Scholar

[36] Shahsavar K, Hosseini M, Shokri E, et al. A sensitive colorimetric aptasensor with a triple-helix molecular switch based on peroxidase-like activity of a dnazyme for ATP detection. Anal Methods, 2017, 9: 4726-4731 CrossRef Google Scholar

[37] Xu J, Wei C. The aptamer DNA-templated fluorescence silver nanoclusters: ATP detection and preliminary mechanism investigation. Biosens Bioelectron, 2017, 87: 422-427 CrossRef Google Scholar

[38] Lu L, Si J C, Gao Z F, et al. Highly selective and sensitive electrochemical biosensor for atp based on the dual strategy integrating the cofactor-dependent enzymatic ligation reaction with self-cleaving DNAzyme-amplified electrochemical detection. Biosens Bioelectron, 2015, 63: 14-20 CrossRef Google Scholar

[39] Kong R M, Zhang X B, Chen Z, et al. Unimolecular Catalytic DNA Biosensor for Amplified Detection ofl-Histidine via an Enzymatic Recycling Cleavage Strategy. Anal Chem, 2011, 83: 7603-7607 CrossRef Google Scholar

[40] He J L, Wu P, Zhu S L, et al. Cleaved dnazyme substrate induced enzymatic cascade for the exponential amplified analysis of l-histidine. Talanta, 2015, 132: 809-813 CrossRef Google Scholar

[41] Jiao X X, Luo H Q, Li N B. Fabrication of graphene–gold nanocomposites by electrochemical co-reduction and their electrocatalytic activity toward 4-nitrophenol oxidation. J Electroanal Chem, 2013, 691: 83-89 CrossRef Google Scholar

[42] Baum D A, Silverman S K. Deoxyribozymes: Useful DNA catalysts in vitro and in vivo. Cell Mol Life Sci, 2008, 65: 2156-2174 CrossRef Google Scholar

[43] Dass C R, Choong P F M, Khachigian L M. DNAzyme technology and cancer therapy: Cleave and let die. Mol Cancer Therapeutics, 2008, 7: 243-251 CrossRef Google Scholar

[44] Cairns M J, Hopkins T M, Witherington C, et al. The influence of arm length asymmetry and base substitution on the activity of the 10–23 DNA enzyme. Antis Nucl A, 2000, 10: 323–332. Google Scholar

[45] Wu Y, Yu L, McMahon R, et al. Inhibition of BCR-ABL oncogene expression by novel deoxyribozymes (DNAzymes). Human Gene Ther, 1999, 10: 2847-2857 CrossRef Google Scholar

[46] Fan H, Zhang X, Lu Y. Recent advances in DNAzyme-based gene silencing. Sci China Chem, 2017, 60: 591-601 CrossRef Google Scholar

[47] Fan H, Zhao Z, Yan G, et al. A Smart DNAzyme-MnO2 Nanosystem for Efficient Gene Silencing. Angew Chem Int Ed, 2015, 54: 4801-4805 CrossRef Google Scholar

[48] Santoro S W, Joyce G F. A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad Sci USA, 1997, 94: 4262-4266 CrossRef ADS Google Scholar

[49] Unwalla H, Banerjea A C. Novel mono- and di-DNA-enzymes targeted to cleave TAT or TAT-REV RNA inhibit HIV-1 gene expression. Antiviral Res, 2001, 51: 127-139 CrossRef Google Scholar

[50] Unwalla H, Banerjea A C. Inhibition of HIV-1 gene expression by novel macrophage-tropic DNA enzymes targeted to cleave HIV-1 TAT/rev RNA. Biochem J, 2001, 357: 147-155 CrossRef Google Scholar

[51] Miao J, Zhang X, Hong Y, et al. Inhibition on hepatitis B virus e-gene expression of 10–23 DNAzyme delivered by novel chitosan oligosaccharide–stearic acid micelles. Carbohydrate Polymers, 2012, 87: 1342-1347 CrossRef Google Scholar

[52] Schubert S. Rna cleaving "10–23" DNAzymes with enhanced stability and activity. Nucl Acids Res, 2003, 31: 5982–5992. Google Scholar